org.jmol.jvxl.readers
Class SurfaceGenerator

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceGenerator

public class SurfaceGenerator
extends java.lang.Object


Field Summary
private  AtomDataServer atomDataServer
           
private  ColorEncoder colorEncoder
           
(package private)  int colorPtr
           
private  JvxlData jvxlData
           
private  MarchingSquares marchingSquares
           
private  MeshData meshData
           
private  MeshDataServer meshDataServer
           
private  Parameters params
           
(package private)  javax.vecmath.Point3f ptRef
           
private  boolean rangeDefined
           
(package private)  javax.vecmath.Vector3f vAB
           
(package private)  javax.vecmath.Vector3f vAC
           
(package private)  javax.vecmath.Vector3f vNorm
           
private  VolumeData volumeData
           
(package private)  VoxelReader voxelReader
           
 
Constructor Summary
SurfaceGenerator()
           
SurfaceGenerator(AtomDataServer atomDataServer, MeshDataServer meshDataServer, ColorEncoder colorEncoder, MeshData meshData, JvxlData jvxlData)
           
 
Method Summary
private  float distanceVerticalToPlane(float x, float y, javax.vecmath.Point3f pta, javax.vecmath.Point3f ptb, javax.vecmath.Point3f ptc)
           
private static float findNearestThreePoints(float x, float y, float[][] xyz, int[] result)
           
private  void generateSurface()
           
(package private)  AtomDataServer getAtomDataServer()
           
 java.util.BitSet getBsIgnore()
           
 java.util.BitSet getBsSelected()
           
 int getColor(int which)
           
(package private)  ColorEncoder getColorEncoder()
           
 float getCutoff()
           
private  void getFunctionZfromXY()
           
 boolean getIAddGridPoints()
           
 boolean getIsPositiveOnly()
           
 boolean getIUseBitSets()
           
 JvxlData getJvxlData()
           
(package private)  MarchingSquares getMarchingSquares()
           
(package private)  MeshData getMeshData()
           
(package private)  MeshDataServer getMeshDataServer()
           
 java.util.Hashtable getMoData()
           
 Parameters getParams()
           
 javax.vecmath.Point4f getPlane()
           
 java.lang.Object getProperty(java.lang.String property, int index)
           
 java.lang.String getScript()
           
 java.lang.String[] getTitle()
           
(package private)  VolumeData getVolumeData()
           
(package private)  void initializeIsosurface()
           
 void initState()
           
 boolean isCubeData()
           
 boolean isInsideOut()
           
 boolean isStateDataRead()
           
private  void mapSurface(java.lang.Object value)
           
private  void processState()
           
(package private)  VoxelReader setFileData(java.lang.Object value)
           
 void setJvxlData(JvxlData jvxlData)
           
 java.lang.String setLcao()
           
(package private)  void setMarchingSquares(MarchingSquares marchingSquares)
           
 void setModelIndex(int modelIndex)
           
 boolean setParameter(java.lang.String propertyName, java.lang.Object value)
          setParameter is the main interface for surface generation.
 boolean setParameter(java.lang.String propertyName, java.lang.Object value, java.util.BitSet bs)
           
private  void setReader()
           
private  void setup(AtomDataServer atomDataServer, MeshDataServer meshDataServer, ColorEncoder colorEncoder, MeshData meshData, JvxlData jvxlData)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

colorEncoder

private ColorEncoder colorEncoder

jvxlData

private JvxlData jvxlData

meshData

private MeshData meshData

params

private Parameters params

volumeData

private VolumeData volumeData

meshDataServer

private MeshDataServer meshDataServer

atomDataServer

private AtomDataServer atomDataServer

marchingSquares

private MarchingSquares marchingSquares

voxelReader

VoxelReader voxelReader

colorPtr

int colorPtr

rangeDefined

private boolean rangeDefined

vAC

final javax.vecmath.Vector3f vAC

vAB

final javax.vecmath.Vector3f vAB

vNorm

final javax.vecmath.Vector3f vNorm

ptRef

final javax.vecmath.Point3f ptRef
Constructor Detail

SurfaceGenerator

public SurfaceGenerator()

SurfaceGenerator

public SurfaceGenerator(AtomDataServer atomDataServer,
                        MeshDataServer meshDataServer,
                        ColorEncoder colorEncoder,
                        MeshData meshData,
                        JvxlData jvxlData)
Method Detail

setup

private void setup(AtomDataServer atomDataServer,
                   MeshDataServer meshDataServer,
                   ColorEncoder colorEncoder,
                   MeshData meshData,
                   JvxlData jvxlData)

isStateDataRead

public boolean isStateDataRead()

getMeshDataServer

MeshDataServer getMeshDataServer()

getAtomDataServer

AtomDataServer getAtomDataServer()

getColorEncoder

ColorEncoder getColorEncoder()

setJvxlData

public void setJvxlData(JvxlData jvxlData)

getJvxlData

public JvxlData getJvxlData()

getMeshData

MeshData getMeshData()

setMarchingSquares

void setMarchingSquares(MarchingSquares marchingSquares)

getMarchingSquares

MarchingSquares getMarchingSquares()

getParams

public Parameters getParams()

getScript

public java.lang.String getScript()

getTitle

public java.lang.String[] getTitle()

getBsSelected

public java.util.BitSet getBsSelected()

getBsIgnore

public java.util.BitSet getBsIgnore()

getVolumeData

VolumeData getVolumeData()

getPlane

public javax.vecmath.Point4f getPlane()

getColor

public int getColor(int which)

setModelIndex

public void setModelIndex(int modelIndex)

getIUseBitSets

public boolean getIUseBitSets()

getIAddGridPoints

public boolean getIAddGridPoints()

getIsPositiveOnly

public boolean getIsPositiveOnly()

isInsideOut

public boolean isInsideOut()

getCutoff

public float getCutoff()

getMoData

public java.util.Hashtable getMoData()

isCubeData

public boolean isCubeData()

setParameter

public boolean setParameter(java.lang.String propertyName,
                            java.lang.Object value)
setParameter is the main interface for surface generation.

Parameters:
propertyName -
value -
Returns:
True if handled; False if not

setParameter

public boolean setParameter(java.lang.String propertyName,
                            java.lang.Object value,
                            java.util.BitSet bs)

processState

private void processState()

setReader

private void setReader()

generateSurface

private void generateSurface()

mapSurface

private void mapSurface(java.lang.Object value)

getProperty

public java.lang.Object getProperty(java.lang.String property,
                                    int index)

setFileData

VoxelReader setFileData(java.lang.Object value)

initializeIsosurface

void initializeIsosurface()

initState

public void initState()

setLcao

public java.lang.String setLcao()

getFunctionZfromXY

private void getFunctionZfromXY()

distanceVerticalToPlane

private float distanceVerticalToPlane(float x,
                                      float y,
                                      javax.vecmath.Point3f pta,
                                      javax.vecmath.Point3f ptb,
                                      javax.vecmath.Point3f ptc)

findNearestThreePoints

private static float findNearestThreePoints(float x,
                                            float y,
                                            float[][] xyz,
                                            int[] result)